Antibiotics are among the most commonly prescribed medicines in the US. In 2010-2011, doctors wrote an estimated 506 antibiotic prescriptions for every 1,000 people each year, of which only about 353 were likely appropriate. When you have a bacterial infection, antibiotics can be lifesaving. But they do not only hit the bacteria making you sick. Here is what they do to your gut, and four practical ways to support it afterward.
What do antibiotics do to your gut?
Your gut is home to tens of trillions of bacteria, roughly as many as there are human cells in your body. They help digest food, train the immune system and protect the gut lining. The gut-associated lymphoid tissue represents almost 70% of the entire immune system, and gut bacteria even help regulate the production of serotonin in the gut.
Antibiotics cannot tell helpful bacteria from harmful ones, so a course can knock back both. In one study of healthy men given a four-day course of three broad-spectrum antibiotics, the gut microbiota recovered to near its original makeup within about six weeks, but nine common species were still undetectable in most participants after six months. The gut is resilient, but the effects can linger, and diarrhea during or after a course is a common side effect.
1. Feed your gut bacteria with fiber
The bacteria that survive need food to repopulate. Fiber, and the prebiotic fibers in particular, resist digestion and reach the colon, where gut bacteria ferment them. Aim for a wide variety of plants: vegetables, fruit, beans and lentils, whole grains, nuts and seeds. Onions, garlic, leeks, asparagus and bananas are good prebiotic sources. Read more in What Are Prebiotics?
While your gut recovers, it also makes sense to cut back on ultra-processed foods and added sugar, which crowd out the fiber-rich foods your gut bacteria rely on.
2. Add fermented foods
Fermented foods such as yogurt, kefir, sauerkraut, kimchi, miso, tempeh and kombucha can contain live bacteria. In a 17-week study, a diet high in fermented foods steadily increased gut microbiome diversity and decreased inflammatory markers. Choose unpasteurized or "live and active cultures" versions where you can, since heat treatment after fermentation kills the bacteria.
3. Consider a probiotic
Probiotics are best supported for preventing problems during an antibiotic course. A 2021 review of 42 trials in more than 11,000 adults found that taking probiotics alongside antibiotics lowered the risk of antibiotic-associated diarrhea by 37%, with the clearest benefit from Lactobacillus and Bifidobacterium species and from higher doses. An earlier review reached a similar conclusion.
If you choose a probiotic, Trust Your Gut High Potency Probiotic delivers 52 billion CFU from 11 acid-resistant strains plus organic prebiotics, and is designed for when you have taken antibiotics or want a gut reset. For everyday use, Trust Your Gut Probiotic + Prebiotic Daily Essential provides 16 billion CFU from 6 strains. Ask your pharmacist how to space probiotic and antibiotic doses, and see How & When to Take Your Probiotic for timing tips. If you are immunocompromised or seriously ill, talk to your doctor before starting any probiotic.
4. Use antibiotics only when you need them
The best way to protect your gut is to avoid antibiotics you do not need. Antibiotics only work against bacterial infections such as strep throat; they do nothing for viral infections like colds and flu. Based on the prescribing figures above, roughly 3 in 10 outpatient antibiotic prescriptions were likely unnecessary.
- Ask your doctor whether your infection is bacterial or viral, and whether an antibiotic is needed.
- When you are prescribed one, take it exactly as directed. Do not swap it for herbal remedies such as garlic or oregano oil.
- Never take leftover antibiotics or someone else's prescription.
Mild digestive changes in the first days of a new probiotic are common and usually settle; our article on possible probiotic side effects explains what is normal. Severe or persistent diarrhea during or after antibiotics needs medical attention.
